Modeling genome-wide by environment interactions through omnigenic interactome networks

Haojie Wang, Meixia Ye, Yaru Fu, Ang Dong, Miaomiao Zhang, Li Feng, Xuli Zhu, Wenhao Bo, Libo Jiang, Christopher H. Griffin, Dan Liang, Rongling Wu

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

How genes interact with the environment to shape phenotypic variation and evolution is a fundamental question intriguing to biologists from various fields. Existing linear models built on single genes are inadequate to reveal the complexity of genotype-environment (G-E) interactions. Here, we develop a conceptual model for mechanistically dissecting G-E interplay by integrating previously disconnected theories and methods. Under this integration, evolutionary game theory, developmental modularity theory, and a variable selection method allow us to reconstruct environment-induced, maximally informative, sparse, and casual multilayer genetic networks. We design and conduct two mapping experiments by using a desert-adapted tree species to validate the biological application of the model proposed. The model identifies previously uncharacterized molecular mechanisms that mediate trees’ response to saline stress. Our model provides a tool to comprehend the genetic architecture of trait variation and evolution and trace the information flow of each gene toward phenotypes within omnigenic networks.

Original languageEnglish (US)
Article number109114
JournalCell Reports
Volume35
Issue number6
DOIs
StatePublished - May 11 2021

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)

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